Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagactgttgttttctcgtcgttttaaatgtttatgttgtgcgtttgatctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ14601
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G064302_T01 (Zea mays), 3'ss of exon 9
----------------------------------------gtagactgttgttttctcgtcgtttta-aatgtttatgttgtgcgtttgatctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG
                                         | ||   | |   ||   |  | | | ||| |   |  |||| |    |  |   | |||||||| |||||||| || ||||| |||||| | || || || |||||||||||||| ||||||
acgctcttttgttttatgttgaccgtagggtacctacaaaatcgatcatcggcatccatttatctcacaatctaatttctgtgtgaaccaa-tatatgcagGAAAACAAAGAAGGCCTTGAACTATTGAAGGCAGCCATAGAAAAGGCTGGCTACACTGGAAAG

upper sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 9
-----------------------------------------gtag-actgttgttttctcgtcgttttaaatgtttatgttgtgcgtttgatctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG
                                          ||   |||||  | |||  | |||  | |   |||| | ||  | | | |    ||| ||||||| ||||||||||| |||||  |||||||||| ||||  || ||||| ||||| ||||||
tgtaatgtaataatccaaatttgtataaaaaattatttttcttactgctgttactgtctgctggttcaatacagttatat-gtttgct-gtttaatttatagGAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG

upper sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------gtagactgttgttttctcgtcgttttaaatgtttatgtt--gtgcgtttga-------tctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG
                                | ||   | | ||| || | |||||  ||    |  ||  |||   ||||       |   || |||||| || | ||||||||||||||||||||||||||| || | |||||| ||||||||||  |||
acgagattgtgtaacttggtacttgtttatattggatattcggtttttccttgttttgtataccaagtttcggtggaattgagacgtgcttgactcacagGATAACAGAGAAGGTCTGGAACTGTTGAAGACTGCCATAGCGAAGGCAGGCTACACCGATAAG

upper sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: PP1S1_526V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------gtagactgttgttt----tctcgtcgtttt--aaatgttt--atgttgtgcgtttgatctg----cttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG
                            |  |||  || ||     ||| || || |   | |||||   |    |     |  | |||    |  |||||| || | ||||||||| ||| || |||||||||| |||| ||||||||||||||| |  |||
tggtatcgctgtactctcggcttttgttggtgacactttttccaaatctggttgtctgggagatgttctaacacggcattgtccacctgggaccacacagGATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169109533|gb|FE514140.1|FE514140
EST:     TAGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTCCAAGTATTCAG                         GAAAATAAAGAAGGTCTGGAACTGTTGAAGAC
genomic: TAGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTCCAAGTATTCAGgtagactgtt ... ctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGAC
EST: gi|169060046|gb|FE468656.1|FE468656
EST:     TAGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTCCAAGTATTCAG                         GAAAATAAGGAAGGTCTGGAACTGTTGAAGAC
genomic: TAGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTCCAAGTATTCAGgtagactgtt ... ctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGAC
EST: gi|169107364|gb|FE508285.1|FE508285
EST:     TAGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTCCAAGTATTCAG                         GAAAATAAAGAAGGTCTGGAACTGTTGAAGAC
genomic: TAGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTCCAAGTATTCAGgtagactgtt ... ctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGAC
EST: gi|169069559|gb|FE476964.1|FE476964
EST:     AGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTCTCA-GTATTCAG                         GAAAATAAGGAAGGTCTGGAACTGTTGAAGAC
genomic: AGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTC-CAAGTATTCAGgtagactgtt ... ctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 40

GCTGTTATCAAGAAGAAATATGGCCTAGACGCCACTAATGTAGGAGACGAGGGTGGTTTTGCTCCAAGTATTCAGgtagactgtt ... ctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgttttctcgtcgttttaaatgtttatgttgtgcgtttgatctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG
                                      gtttgat  putative branch site (score: 40)
                                            tctgctt  CT-rich tract
                 ttttaaatgtttatgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagactgttgttttctcgtcgttttaaatgtttatgttgtgcgtttgatctgcttacagGAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA